An apparatus for supplementing a brake vacuum pressure may include an engine control unit (ECU) that generates a vacuum pressure control signal for supplementing the brake vacuum pressure in accordance with the result of determining whether the brake vacuum pressure is included in a reference vacuum pressure range after a vehicle implements an ISG process, a sub-oil pump that is operated in accordance with a control signal from the ECU to supply hydraulic pressure to the inside of an automatic transmission after the vehicle implements the ISG process, a vacuum pump that generates and supplies the brake vacuum pressure to a brake system, and an electronic clutch that selectively couples the sub-oil pump and the vacuum pump to allow driving force of the sub-oil pump to be transmitted to the vacuum pump or to be cut, in accordance with whether the vacuum pressure control signal is sent thereto.